WASHINGTON — Congressional negotiators introduced a sweeping year-end spending and tax-break package early Wednesday that busts through previously agreed budget limits with $66 billion in new spending for 2016 and that makes permanent an array of tax benefits at a cost of adding more than a half-trillion dollars to the deficit.

The $1.1 trillion spending measure includes a provision to end the 40-year ban on exports of crude oil from the United States — a major priority of Republicans — and also provides a large increase in funds for medical research at the National Institutes of Health. It also reauthorizes and expands federal aid for emergency workers suffering from health ailments related to the Sept. 11 terrorist attacks in New York City.

After weeks of tense negotiations, congressional Democrats and the White House succeeded in beating back policy amendments that Republicans had sought to attach to the spending measure. Those included efforts to scuttle an environmental rule expanding federal oversight over domestic waterways, new conflict of interest rules for financial advisers and a labor provision that would have made it more difficult for employees of fast-food restaurants to join unions.

The spending bill also includes new restrictions to the visa-waiver program, a fast-track process used by millions of visitors to enter the United States, that lawmakers pursued because of concern after the recent terrorist attacks carried out by the Islamic State. The bill also incorporates a measure that expands the sharing of information between private firms and federal security agencies to prevent cyberattacks.

The spending measure notably does not include tighter restrictions on admitting Syrian and Iraqi refugees that had been approved overwhelmingly in a separate measure in the House; the Obama administration and Senate Democrats said they would block it if added.

The tax portion also delays some important provisions of the Affordable Care Act, including the so-called Cadillac tax on expensive private health insurance plans.

While Republican leaders in Congress characterized the year-end package as representing a hard-fought compromise that would keep the government open and provide large-scale investment and tax breaks, it poses a challenge for Speaker Paul D. Ryan, Republican of Wisconsin, who had promised a more open and inclusive legislative process.

Republicans posted the spending measure, which contains 2,009 pages, at 1:34 a.m., missing a midnight deadline. That forced Mr. Ryan to delay a vote on the proposal that he had initially planned for Thursday.

Some conservatives immediately complained that they were once again rushed into making a decision on major legislation. The 233-page tax measure was released just before midnight, and House leaders said a Thursday vote on that portion would proceed as planned. Still, Mr. Ryan was left effectively apologizing, and described himself as equally annoyed by the way the process had played out.

“Let me be the first to say, I don’t think this is the way government should work,” Mr. Ryan said at a news conference Wednesday morning at the Capitol. “This is not how appropriations should work.”

The House is expected to vote on the spending bill on Friday, then go to the Senate where the two measures may be combined into a single piece of legislation.

While the overall deal is expected to be approved, shepherding the package into law will not be easy.

The votes of House Democrats are almost certainly needed to pass the spending measure, but many of them oppose the tax package. Many Republicans support the tax cuts, but some conservatives object to the additional deficit spending.

The House Democratic leader, Representative Nancy Pelosi, of California, voiced outrage on Wednesday over the tax-break bill, which she said would unfairly benefit big business over the middle-class and working-poor Americans. At a brief news conference, she called it “practically an immorality.”

In the Senate, the majority leader, Mitch McConnell, Republican of Kentucky, urged his colleagues to read the legislation and prepare for debate.

The Senate Democratic leader, Harry Reid of Nevada, said, “This was not an easy process,” but noted, “no legislation is perfect. This is good legislation that is truly the art of compromise.”

At the White House on Wednesday, the press secretary, Josh Earnest, praised the result, suggesting that Mr. Obama would sign the package into law. Mr. Earnest happily listed the many riders championed by Republicans that he had been asked about repeatedly in recent weeks that were not in the final legislation, including provisions to curtail the Dodd-Frank financial industry regulation law and an effort to cut off financing for Planned Parenthood.

“We feel good about the outcome,” Mr. Earnest said, adding: “The president would be pleased to sign the bill.”

To get to that point, however, Congress will need to extend a stopgap spending measure that has kept the government functioning since Friday, when lawmakers missed an initial deadline to complete the spending package. Congressional leaders said they would keep the stopgap in place until Tuesday.

Mr. Ryan said he hoped to begin the regular appropriations process early next year, offering enough time to debate the bills. A budget agreement reached in October with Democrats and the White House may make that easier, but the current negotiations showed that even with overall spending limits set, Democrats and Republicans have such fundamentally different views that it is difficult to find consensus on anything but the most basic priorities of government.

Mr. Ryan also noted that he had become speaker at a point when negotiations over the omnibus spending bill had already begun between Democrats and his predecessor, John A. Boehner, Republican of Ohio.

“We played the cards that we were dealt with as best as we possibly could,” Mr. Ryan said. “I believe we’ve made the best of it.”

For weeks, negotiations focused on the policy changes, or so-called riders that lawmakers in both parties — especially Republicans seeking to thwart the Obama administration — had hoped to attach to the spending measure.

Democrats, for their part, had hoped for a rider that would have ended a ban on federal financing for medical research into gun violence. No riders related to gun control are in the bill.

One area of notable compromise was the increase in financing for the National Institutes of Health, by $2 billion.

Health advocates applauded the increase for N.I.H., which saw funding decline several years ago under budget cuts commonly referred to as the sequester. Researchers complained that the cuts delayed grants and made it more difficult to do government-funded scientific work in the United States.

“This is huge,” said Christopher W. Hansen, president of the American Cancer Society Cancer Action Network, an advocacy group. He said the increase restored the cuts that were part of the budget controls, and increased N.I.H. funding by an additional 4 percent. “We’re going to have a lot of people who will survive because of this.”